Untangling Molecular Biodiversity

Towards Eradicating the Nuisance of Numts and Noise in Molecular Biodiversity Assessment

Molecular Ecology Resources ◽

10.1111/1755-0998.13414 ◽

2021 ◽

Author(s):

Natalie R. Graham ◽

Rosemary G. Gillespie ◽

Henrik Krehenwinkel

Keyword(s):

Biodiversity Assessment ◽

Molecular Biodiversity

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Sequence Analysis and Classification of Apparent Recombinant Begomoviruses Infecting Tomato in the Nile and Mediterranean Basins

Phytopathology ◽

10.1094/phyto-95-0549 ◽

2005 ◽

Vol 95 (5) ◽

pp. 549-555 ◽

Cited By ~ 48

Author(s):

C. M. Fauquet ◽

S. Sawyer ◽

A. M. Idris ◽

J. K. Brown

Keyword(s):

Sequence Analysis ◽

Phylogenetic Relationships ◽

Tomato Yellow Leaf ◽

Viral Diseases ◽

Yellow Leaf ◽

Recombination Hotspots ◽

Molecular Biodiversity ◽

Leaf Curl Virus ◽

Leaf Curl

Numerous whitefly-transmitted viral diseases of tomato have emerged in countries around the Nile and Mediterranean Basins the last 20 years. These diseases are caused by monopartite geminiviruses (family Gemini viridae) belonging to the genus Begomovirus that probably resulted from numerous recombination events. The molecular biodiversity of these viruses was investigated to better appreciate the role and importance of recombination and to better clarify the phylogenetic relationships and classification of these viruses. The analysis partitioned the tomato-infecting begomoviruses from this region into two major clades, Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus. Phylogenetic and pairwise analyses together with an evaluation for gene conversion were performed from which taxonomic classification and virus biodiversity conclusions were drawn. Six recombination hotspots and three homogeneous zones within the genome were identified among the tomatoinfecting isolates and species examined here, suggesting that the recombination events identified were not random occurrences.

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MBlab: Molecular Biodiversity Laboratory

Communications in Computer and Information Science - Digital Libraries and Archives ◽

10.1007/978-3-642-27302-5_18 ◽

2011 ◽

pp. 132-135

Author(s):

Corrado Loglisci ◽

Annalisa Appice ◽

Michelangelo Ceci ◽

Donato Malerba ◽

Floriana Esposito

Keyword(s):

Molecular Biodiversity

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Suggestions for a molecular biodiversity assessment of South East Asian freshwater invertebrates. Lessons from the megadiverse beetles (Coleoptera)

Journal of Limnology ◽

10.4081/jlimnol.2013.s2.e4 ◽

2013 ◽

Vol 72 (s2) ◽

Cited By ~ 4

Author(s):

Michael Balke ◽

Lars Hendrich ◽

Emmanuel F.A. Toussaint ◽

Xin Zhou ◽

Thomas Von Rintelen ◽

...

Keyword(s):

East Asian ◽

Biodiversity Assessment ◽

Freshwater Invertebrates ◽

Molecular Biodiversity

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Faculty Opinions recommendation of Molecular biodiversity of arbuscular mycorrhizal fungi in trace metal-polluted soils.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13199982.14542095 ◽

2011 ◽

Author(s):

Nico M van Straalen

Keyword(s):

Arbuscular Mycorrhizal Fungi ◽

Trace Metal ◽

Mycorrhizal Fungi ◽

Arbuscular Mycorrhizal ◽

Polluted Soils ◽

Molecular Biodiversity

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Methodological constraints in the molecular biodiversity study of a thermomineral spring cyanobacterial mat: a case study

Antonie van Leeuwenhoek ◽

10.1007/s10482-010-9486-5 ◽

2010 ◽

Vol 99 (2) ◽

pp. 271-281 ◽

Cited By ~ 7

Author(s):

Cristian Coman ◽

Adriana Bica ◽

Bogdan Drugă ◽

Lucian Barbu-Tudoran ◽

Nicolae Dragoş

Keyword(s):

Cyanobacterial Mat ◽

Molecular Biodiversity ◽

Biodiversity Study

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Molecular biodiversity assessment of plant-parasitic nematodes in Dokdo Island, Korea

Nematology ◽

10.1163/15685411-00003213 ◽

2019 ◽

Vol 21 (3) ◽

pp. 275-292 ◽

Cited By ~ 1

Author(s):

Dongwoo Kim ◽

Hwal-Su Hwang ◽

Jae-Kyoung Shim ◽

JiYoung Yang ◽

Jae Hong Pak ◽

...

Keyword(s):

Parasitic Nematode ◽

Rhizosphere Soil ◽

Soil Samples ◽

Parasitic Nematodes ◽

Biodiversity Assessment ◽

Plant Parasitic Nematodes ◽

Species Diagnosis ◽

Molecular Biodiversity ◽

Natural Monument ◽

Plant Parasitic

Summary Dokdo Island has a unique biodiversity that has been preserved as a natural monument. Although the biodiversity of Dokdo has been investigated, little information is available regarding the nematodes. The diversity of plant-parasitic nematodes was investigated using both ITS and D2-D3 sequences. Nematodes extracted from 59 rhizosphere soil samples were morphologically identified as belonging to eight genera: Geocenamus, Helicotylenchus, Rotylenchulus, Heterodera, Paratylenchus, Pratylenchus, Pratylenchoides and Xiphinema. Further, nucleotide sequences were determined from 85 individuals of different genera for species diagnosis. We identified 13 species, including three species of the genus Pratylenchus (P. crenatus, P. kumamotoensis and P. neglectus), Helicotylenchus sp. 1, Rotylenchulus sp. 1, Paratylenchus nanus, Heterodera trifolii, Heterodera spp., Pratylenchoides ritteri, Geocenamus sp. 1, Geocenamus sp. 2, Xiphinema brevicollum and Xiphinema sp. 1. The dominant plant-parasitic nematode on Dokdo was P. crenatus, which was found in 25.4% of the samples. Our study provides important information about the biodiversity of plant-parasitic nematodes on Dokdo Island.

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